Place a saute pan over medium high heat with 1 tablespoon olive oil. Add in chopped onions.
Once the onions start browning, add garlic, zucchini, kale, and red pepper. Saute for about 4 minutes or until the vegetables are fully cooked. Season with a bit of salt.
Place the remaining 1 tablespoon olive oil in a sauce pan over medium high heat.
Once the oil is heated, add the coconut flour and mix.
When the oil and flour starts to bubble a little, pour in milk.
Add the mozzarella and parmesan cheese when the milk bubbles.
Stir until the cheese melts.
Add in basil (and any other dried herbs) into the cheese mixture and stir.
Pour the cheese mixture into the bowl with the spaghetti squash and mix.
Fold in the sauteed vegetables with the spaghetti squash.
Season with salt and pepper, if necessary.